Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate Ac3H11_3326 Amino acid ABC transporter, permease protein
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3326 Length = 260 Score = 105 bits (261), Expect = 2e-27 Identities = 79/246 (32%), Positives = 120/246 (48%), Gaps = 16/246 (6%) Query: 142 NAILLFAV-LPVIAFWLLHGGFGLEVVETPLWG-------GLMVTLVLSFVGIAVSLPVG 193 NA L+ AV L V+A LL G L + P+ G TL L+ + +V L +G Sbjct: 17 NATLVSAVILMVLALALL--GQLLSFLPEPIGSNAQAFSDGARTTLWLTLISGSVGLVLG 74 Query: 194 ILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLLRALIG 253 AL R +R V+R +I VIRG PL+ + LP+ +P G N+ A++ Sbjct: 75 TGAALARTARWAVVRWAASFYIWVIRGTPLLVQILFVYFALPVLVP-GLNLPDFAAAVLA 133 Query: 254 VSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIVNTFI 313 + + AY AE IR GL A+P+GQ E A +LGLG ++ PQA K+ +P +V+ F+ Sbjct: 134 LGLNVGAYNAEAIRAGLLAVPRGQTEAAKALGLGRMHVFFDVVFPQAFKISLPPLVSNFV 193 Query: 314 GTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMSRYSGF 373 KD+SL IG+ +L N + ++ PI L + L +++ S Sbjct: 194 ALLKDSSLAYAIGVVEL-----TNVGNRIQSATFQPIATLSTVAITYLLLTTLVTQISNA 248 Query: 374 MERHLD 379 +E D Sbjct: 249 VEYRFD 254 Score = 30.4 bits (67), Expect = 6e-05 Identities = 39/139 (28%), Positives = 57/139 (41%), Gaps = 20/139 (14%) Query: 41 VILTILALALIAWAVPHLVNWLF--IQAVWSGPDRTFCATTLQGGIQPDGWSGAC----- 93 VIL +LALAL+ + L + QA G T T + G + +GA Sbjct: 24 VILMVLALALLGQLLSFLPEPIGSNAQAFSDGARTTLWLTLISGSVGLVLGTGAALARTA 83 Query: 94 -WAFISAKYDQFIFGRYPLGERWRPAIVGILFILLLVPMLIPSAPRKGLNAILLFAVLPV 152 WA + +I+ R P +V ILF+ +P+L+P GLN L V Sbjct: 84 RWAVVRWAASFYIWVI-----RGTPLLVQILFVYFALPVLVP-----GLN--LPDFAAAV 131 Query: 153 IAFWLLHGGFGLEVVETPL 171 +A L G + E + L Sbjct: 132 LALGLNVGAYNAEAIRAGL 150 Lambda K H 0.330 0.145 0.469 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 259 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 384 Length of database: 260 Length adjustment: 27 Effective length of query: 357 Effective length of database: 233 Effective search space: 83181 Effective search space used: 83181 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory